Hi Freesurfer experts,
I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, gender is not showing up as a covariate variable or a nuisance factor (only showing up as a fixed factor), I am wondering how I could control for gender in this case?
Thank you very much,
Jen
Just include it as a categorical factor. When you look at your contrast of interest, it will be with respect to regressing out gender
On 01/15/2017 08:55 PM, Jennifer Szeto wrote:
Hi Freesurfer experts,
I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, _gender_ is not showing up as a covariate variable or a nuisance factor (only showing up as a fixed factor), I am wondering how I could control for gender in this case?
Thank you very much,
Jen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug,
That seem to work for some of my variables (e.g. depression) when I put gender and diagnosis as fixed factors, depression as covariate, and age as nuisance factor but not for others (e.g. anxiety). I keep getting error messages when trying to run some of my variables as covariates (please see attached). Is there anything I can do to fix this?
Thanks, Jen
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: 19 January 2017 21:48 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC - Controlling for gender
Just include it as a categorical factor. When you look at your contrast of interest, it will be with respect to regressing out gender
On 01/15/2017 08:55 PM, Jennifer Szeto wrote:
Hi Freesurfer experts,
I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, _gender_ is not showing up as a covariate variable or a nuisance factor (only showing up as a fixed factor), I am wondering how I could control for gender in this case?
Thank you very much,
Jen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard Universityhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 FileDrop v2.0 - Martinos Center for Biomedical Imaginghttps://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Martinos Center File Drophttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
can you send the fsgd file?
On 1/20/17 6:54 AM, Jennifer Szeto wrote:
Thanks Doug,
That seem to work for some of my variables (e.g. depression) when I put gender and diagnosis as fixed factors, depression as covariate, and age as nuisance factor but not for others (e.g. anxiety). I keep getting error messages when trying to run some of my variables as covariates (please see attached). Is there anything I can do to fix this?
Thanks, Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* 19 January 2017 21:48 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender Just include it as a categorical factor. When you look at your contrast of interest, it will be with respect to regressing out gender
On 01/15/2017 08:55 PM, Jennifer Szeto wrote:
Hi Freesurfer experts,
I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, _gender_ is not showing up as a covariate variable or a nuisance factor (only showing up as a fixed factor), I am wondering how I could control for gender in this case?
Thank you very much,
Jen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard University https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you very much Doug,
Please find attached the files I have been using to run the QDEC analyses.
Jen
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Sent: 20 January 2017 15:27 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC - Controlling for gender
can you send the fsgd file?
On 1/20/17 6:54 AM, Jennifer Szeto wrote:
Thanks Doug,
That seem to work for some of my variables (e.g. depression) when I put gender and diagnosis as fixed factors, depression as covariate, and age as nuisance factor but not for others (e.g. anxiety). I keep getting error messages when trying to run some of my variables as covariates (please see attached). Is there anything I can do to fix this?
Thanks, Jen
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Sent: 19 January 2017 21:48 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC - Controlling for gender
Just include it as a categorical factor. When you look at your contrast of interest, it will be with respect to regressing out gender
On 01/15/2017 08:55 PM, Jennifer Szeto wrote:
Hi Freesurfer experts,
I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, _gender_ is not showing up as a covariate variable or a nuisance factor (only showing up as a fixed factor), I am wondering how I could control for gender in this case?
Thank you very much,
Jen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard Universityhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 FileDrop v2.0 - Martinos Center for Biomedical Imaginghttps://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Martinos Center File Drophttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.eduhttp://www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sorry, I wanted the y.fsgd file from the qdec output directory
On 1/20/17 4:46 PM, Jennifer Szeto wrote:
Thank you very much Doug,
Please find attached the files I have been using to run the QDEC analyses.
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* 20 January 2017 15:27 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
can you send the fsgd file?
On 1/20/17 6:54 AM, Jennifer Szeto wrote:
Thanks Doug,
That seem to work for some of my variables (e.g. depression) when I put gender and diagnosis as fixed factors, depression as covariate, and age as nuisance factor but not for others (e.g. anxiety). I keep getting error messages when trying to run some of my variables as covariates (please see attached). Is there anything I can do to fix this?
Thanks, Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* 19 January 2017 21:48 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender Just include it as a categorical factor. When you look at your contrast of interest, it will be with respect to regressing out gender
On 01/15/2017 08:55 PM, Jennifer Szeto wrote:
Hi Freesurfer experts,
I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, _gender_ is not showing up as a covariate variable or a nuisance factor (only showing up as a fixed factor), I am wondering how I could control for gender in this case?
Thank you very much,
Jen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard University https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, hope this is the right one!
Thanks,
Jen
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Sent: 20 January 2017 22:26 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC - Controlling for gender
sorry, I wanted the y.fsgd file from the qdec output directory
On 1/20/17 4:46 PM, Jennifer Szeto wrote:
Thank you very much Doug,
Please find attached the files I have been using to run the QDEC analyses.
Jen
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Sent: 20 January 2017 15:27 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC - Controlling for gender
can you send the fsgd file?
On 1/20/17 6:54 AM, Jennifer Szeto wrote:
Thanks Doug,
That seem to work for some of my variables (e.g. depression) when I put gender and diagnosis as fixed factors, depression as covariate, and age as nuisance factor but not for others (e.g. anxiety). I keep getting error messages when trying to run some of my variables as covariates (please see attached). Is there anything I can do to fix this?
Thanks, Jen
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Sent: 19 January 2017 21:48 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC - Controlling for gender
Just include it as a categorical factor. When you look at your contrast of interest, it will be with respect to regressing out gender
On 01/15/2017 08:55 PM, Jennifer Szeto wrote:
Hi Freesurfer experts,
I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, _gender_ is not showing up as a covariate variable or a nuisance factor (only showing up as a fixed factor), I am wondering how I could control for gender in this case?
Thank you very much,
Jen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard Universityhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 FileDrop v2.0 - Martinos Center for Biomedical Imaginghttps://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Martinos Center File Drophttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.eduhttp://www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Have you tried normalizing BDI and age? By normalizing, I mean subtracting the mean and dividing by the stddev
On 01/20/2017 05:46 PM, Jennifer Szeto wrote:
Sorry, hope this is the right one!
Thanks,
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* 20 January 2017 22:26 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
sorry, I wanted the y.fsgd file from the qdec output directory
On 1/20/17 4:46 PM, Jennifer Szeto wrote:
Thank you very much Doug,
Please find attached the files I have been using to run the QDEC analyses.
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* 20 January 2017 15:27 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
can you send the fsgd file?
On 1/20/17 6:54 AM, Jennifer Szeto wrote:
Thanks Doug,
That seem to work for some of my variables (e.g. depression) when I put gender and diagnosis as fixed factors, depression as covariate, and age as nuisance factor but not for others (e.g. anxiety). I keep getting error messages when trying to run some of my variables as covariates (please see attached). Is there anything I can do to fix this?
Thanks, Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* 19 January 2017 21:48 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender Just include it as a categorical factor. When you look at your contrast of interest, it will be with respect to regressing out gender
On 01/15/2017 08:55 PM, Jennifer Szeto wrote:
Hi Freesurfer experts,
I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, _gender_ is not showing up as a covariate variable or a nuisance factor (only showing up as a fixed factor), I am wondering how I could control for gender in this case?
Thank you very much,
Jen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard University https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
That doesn't seem to work either....? Is there anything else I should try/ does my fsgd file look alright?
Thanks for your help,
Jen
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: 24 January 2017 04:28 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC - Controlling for gender
Have you tried normalizing BDI and age? By normalizing, I mean subtracting the mean and dividing by the stddev
On 01/20/2017 05:46 PM, Jennifer Szeto wrote:
Sorry, hope this is the right one!
Thanks,
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* 20 January 2017 22:26 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
sorry, I wanted the y.fsgd file from the qdec output directory
On 1/20/17 4:46 PM, Jennifer Szeto wrote:
Thank you very much Doug,
Please find attached the files I have been using to run the QDEC analyses.
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* 20 January 2017 15:27 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
can you send the fsgd file?
On 1/20/17 6:54 AM, Jennifer Szeto wrote:
Thanks Doug,
That seem to work for some of my variables (e.g. depression) when I put gender and diagnosis as fixed factors, depression as covariate, and age as nuisance factor but not for others (e.g. anxiety). I keep getting error messages when trying to run some of my variables as covariates (please see attached). Is there anything I can do to fix this?
Thanks, Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* 19 January 2017 21:48 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender Just include it as a categorical factor. When you look at your contrast of interest, it will be with respect to regressing out gender
On 01/15/2017 08:55 PM, Jennifer Szeto wrote:
Hi Freesurfer experts,
I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, _gender_ is not showing up as a covariate variable or a nuisance factor (only showing up as a fixed factor), I am wondering how I could control for gender in this case?
Thank you very much,
Jen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - mail.nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
Freesurfer Info Page - Harvard University https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - mail.nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
FileDrop v2.0 - Martinos Center for Biomedical Imaginghttps://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2
FileDrop v2.0 - Martinos Center for Biomedical Imaginghttps://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Martinos Center File Drophttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Martinos Center File Drophttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Martinos Center File Drophttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
www.nmr.mgh.harvard.eduhttp://www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
From: Jennifer Szeto jennifer_szeto@hotmail.com Sent: 24 January 2017 23:31 To: Freesurfer support list Subject: Re: [Freesurfer] QDEC - Controlling for gender
Hi Doug,
That doesn't seem to work either....? Is there anything else I should try/ does my fsgd file look alright?
Thanks for your help,
Jen
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: 24 January 2017 04:28 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC - Controlling for gender
Have you tried normalizing BDI and age? By normalizing, I mean subtracting the mean and dividing by the stddev
On 01/20/2017 05:46 PM, Jennifer Szeto wrote:
Sorry, hope this is the right one!
Thanks,
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* 20 January 2017 22:26 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
sorry, I wanted the y.fsgd file from the qdec output directory
On 1/20/17 4:46 PM, Jennifer Szeto wrote:
Thank you very much Doug,
Please find attached the files I have been using to run the QDEC analyses.
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* 20 January 2017 15:27 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
can you send the fsgd file?
On 1/20/17 6:54 AM, Jennifer Szeto wrote:
Thanks Doug,
That seem to work for some of my variables (e.g. depression) when I put gender and diagnosis as fixed factors, depression as covariate, and age as nuisance factor but not for others (e.g. anxiety). I keep getting error messages when trying to run some of my variables as covariates (please see attached). Is there anything I can do to fix this?
Thanks, Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* 19 January 2017 21:48 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender Just include it as a categorical factor. When you look at your contrast of interest, it will be with respect to regressing out gender
On 01/15/2017 08:55 PM, Jennifer Szeto wrote:
Hi Freesurfer experts,
I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, _gender_ is not showing up as a covariate variable or a nuisance factor (only showing up as a fixed factor), I am wondering how I could control for gender in this case?
Thank you very much,
Jen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - mail.nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
Freesurfer Info Page - Harvard University https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - mail.nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
FileDrop v2.0 - Martinos Center for Biomedical Imaginghttps://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2
FileDrop v2.0 - Martinos Center for Biomedical Imaginghttps://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Martinos Center File Drophttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Martinos Center File Drophttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Martinos Center File Drophttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
www.nmr.mgh.harvard.eduhttp://www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the
FileDrop v2.0 - Martinos Center for Biomedical Imaginghttps://gate.nmr.mgh.harvard.edu/filedrop2/ gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
Martinos Center file drop area.
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I just tried normalizing the BDI and age on the fsgd file that you sent, and it did work. Can you double check? If it is still not working, then send both the fsgd file and the Xg.dat file
On 01/27/2017 05:06 PM, Jennifer Szeto wrote:
*From:*Jennifer Szeto jennifer_szeto@hotmail.com *Sent:* 24 January 2017 23:31 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
Hi Doug,
That doesn't seem to work either....? Is there anything else I should try/ does my fsgd file look alright?
Thanks for your help,
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* 24 January 2017 04:28 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender Have you tried normalizing BDI and age? By normalizing, I mean subtracting the mean and dividing by the stddev
On 01/20/2017 05:46 PM, Jennifer Szeto wrote:
Sorry, hope this is the right one!
Thanks,
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* 20 January 2017 22:26 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
sorry, I wanted the y.fsgd file from the qdec output directory
On 1/20/17 4:46 PM, Jennifer Szeto wrote:
Thank you very much Doug,
Please find attached the files I have been using to run the QDEC analyses.
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* 20 January 2017 15:27 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
can you send the fsgd file?
On 1/20/17 6:54 AM, Jennifer Szeto wrote:
Thanks Doug,
That seem to work for some of my variables (e.g. depression) when I put gender and diagnosis as fixed factors, depression as covariate, and age as nuisance factor but not for others (e.g. anxiety). I keep getting error messages when trying to run some of my variables as covariates (please see attached). Is there anything I can do to fix this?
Thanks, Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* 19 January 2017 21:48 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender Just include it as a categorical factor. When you look at your
contrast
of interest, it will be with respect to regressing out gender
On 01/15/2017 08:55 PM, Jennifer Szeto wrote:
Hi Freesurfer experts,
I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, _gender_ is not showing up as a covariate variable or a nuisance factor (only
showing
up as a fixed factor), I am wondering how I could control for gender in this case?
Thank you very much,
Jen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - mail.nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
Freesurfer Info Page - Harvard University https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - mail.nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
https://gate.nmr.mgh.harvard.edu/filedrop2 FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2
FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
www.nmr.mgh.harvard.edu http://www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/
https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2/ gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
Martinos Center file drop area.
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you very much Doug!
It works when I include only normalized age and BDI in the qdec.table.dat file, but not when I include also all the other variables of interest in the file.
As normalizing works for BDI, will I have to normalize all the variables of interest as well? Or just the ones that gives an error message?
Thanks, Jen
On 31 Jan. 2017, at 4:18 am, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
I just tried normalizing the BDI and age on the fsgd file that you sent, and it did work. Can you double check? If it is still not working, then send both the fsgd file and the Xg.dat file
On 01/27/2017 05:06 PM, Jennifer Szeto wrote:
*From:*Jennifer Szeto jennifer_szeto@hotmail.com *Sent:* 24 January 2017 23:31 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
Hi Doug,
That doesn't seem to work either....? Is there anything else I should try/ does my fsgd file look alright?
Thanks for your help,
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* 24 January 2017 04:28 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender Have you tried normalizing BDI and age? By normalizing, I mean subtracting the mean and dividing by the stddev
On 01/20/2017 05:46 PM, Jennifer Szeto wrote:
Sorry, hope this is the right one!
Thanks,
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* 20 January 2017 22:26 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
sorry, I wanted the y.fsgd file from the qdec output directory
On 1/20/17 4:46 PM, Jennifer Szeto wrote:
Thank you very much Doug,
Please find attached the files I have been using to run the QDEC analyses.
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* 20 January 2017 15:27 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
can you send the fsgd file?
On 1/20/17 6:54 AM, Jennifer Szeto wrote:
Thanks Doug,
That seem to work for some of my variables (e.g. depression) when I put gender and diagnosis as fixed factors, depression as covariate, and age as nuisance factor but not for others (e.g. anxiety). I keep getting error messages when trying to run some of my variables as covariates (please see attached). Is there anything I can do to fix this?
Thanks, Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* 19 January 2017 21:48 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender Just include it as a categorical factor. When you look at your
contrast
of interest, it will be with respect to regressing out gender
On 01/15/2017 08:55 PM, Jennifer Szeto wrote:
Hi Freesurfer experts,
I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, _gender_ is not showing up as a covariate variable or a nuisance factor (only
showing
up as a fixed factor), I am wondering how I could control for gender in this case?
Thank you very much,
Jen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - mail.nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
Freesurfer Info Page - Harvard University https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - mail.nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
https://gate.nmr.mgh.harvard.edu/filedrop2 FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2
FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
www.nmr.mgh.harvard.edu http://www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/
https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2/ gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
Martinos Center file drop area.
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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I'd probably normalize everyting
On 2/1/17 7:44 AM, Jennifer Szeto wrote:
Thank you very much Doug!
It works when I include only normalized age and BDI in the qdec.table.dat file, but not when I include also all the other variables of interest in the file.
As normalizing works for BDI, will I have to normalize all the variables of interest as well? Or just the ones that gives an error message?
Thanks, Jen
On 31 Jan. 2017, at 4:18 am, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
I just tried normalizing the BDI and age on the fsgd file that you sent, and it did work. Can you double check? If it is still not working, then send both the fsgd file and the Xg.dat file
On 01/27/2017 05:06 PM, Jennifer Szeto wrote:
*From:*Jennifer Szeto jennifer_szeto@hotmail.com *Sent:* 24 January 2017 23:31 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
Hi Doug,
That doesn't seem to work either....? Is there anything else I should try/ does my fsgd file look alright?
Thanks for your help,
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* 24 January 2017 04:28 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender Have you tried normalizing BDI and age? By normalizing, I mean subtracting the mean and dividing by the stddev
On 01/20/2017 05:46 PM, Jennifer Szeto wrote:
Sorry, hope this is the right one!
Thanks,
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* 20 January 2017 22:26 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
sorry, I wanted the y.fsgd file from the qdec output directory
On 1/20/17 4:46 PM, Jennifer Szeto wrote:
Thank you very much Doug,
Please find attached the files I have been using to run the QDEC analyses.
Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* 20 January 2017 15:27 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender
can you send the fsgd file?
On 1/20/17 6:54 AM, Jennifer Szeto wrote:
Thanks Doug,
That seem to work for some of my variables (e.g. depression) when I put gender and diagnosis as fixed factors, depression as covariate, and age as nuisance factor but not for others (e.g. anxiety). I keep getting error messages when trying to run some of my variables as covariates (please see attached). Is there anything I can do to fix this?
Thanks, Jen
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* 19 January 2017 21:48 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] QDEC - Controlling for gender Just include it as a categorical factor. When you look at your
contrast
of interest, it will be with respect to regressing out gender
> On 01/15/2017 08:55 PM, Jennifer Szeto wrote: > > Hi Freesurfer experts, > > > I am trying to compare cortical thickness between groups while > controlling for age and gender using QDEC. However, _gender_ is not > showing up as a covariate variable or a nuisance factor (only
showing
> up as a fixed factor), I am wondering how I could control for gender > in this case? > > > Thank you very much, > > Jen > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - mail.nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
Freesurfer Info Page - Harvard University https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - mail.nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
https://gate.nmr.mgh.harvard.edu/filedrop2 FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2
FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
www.nmr.mgh.harvard.edu http://www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/
https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2/ gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
Martinos Center file drop area.
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
Jennifer Szeto